+ Click here to see what our final sbatch
code script for collecting the tumor sample alignment metrics should look like
+
+
+```
+#!/bin/bash
+# This sbatch script is for collecting alignment metrics using Picard
+
+# Assign sbatch directives
+#SBATCH -p priority
+#SBATCH -t 0-00:30:00
+#SBATCH -c 1
+#SBATCH --mem 16G
+#SBATCH -o picard_metrics_tumor_%j.out
+#SBATCH -e picard_metrics_tumor_%j.err
+
+# Load picard
+module load picard/2.27.5
+
+# Assign variables
+INPUT_BAM=/n/scratch/users/${USER:0:1}/${USER}/variant_calling/alignments/syn3_tumor_GRCh38.p7.coordinate_sorted.bam
+REFERENCE=/n/groups/hbctraining/variant_calling/reference/GRCh38.p7.fa
+OUTPUT_METRICS_FILE=/home/${USER}/variant_calling/reports/picard/syn3_tumor/syn3_tumor_GRCh38.p7.CollectAlignmentSummaryMetrics.txt
+
+# Run Picard CollectAlignmentSummaryMetrics
+java -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics \
+ --INPUT $INPUT_BAM \
+ --REFERENCE_SEQUENCE $REFERENCE \
+ --OUTPUT $OUTPUT_METRICS_FILE
+```
+
+
+
+
Before we submit our jobs, let's **check the status of our previous `Picard` alignment processing steps**:
```